> > See the 'cluster' command for ptraj or cpptraj. Note that currently
> > ptraj clustering has far more options than cpptraj. Refer to the
> > AmberTools manual for more details.

> How to use the 'cluster' command?
> and what would be the output files?

We expect users to invest a fair amount of effort before asking people on the
list to spend their time in replies. People are willing to help for reports
like "I read Section xxx of the manual, but I don't understand this
sentence...", or "I tried the following calculation, but I got a strange
result....". [Even better is with the addition: "I searched the Amber mail
archives and Googled the error message, but could not find the help I
needed."]

Just asking people on the list to tell you what is already in the Reference
Manual is not a good use of anyone's time.